COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs

Pangenome graphs capture extensive structural diversity, but resolving complex loci from shallow sequencing remains challenging, particularly when samples are of low quality such as in ancient DNA. We introduce COSIGT (COsine SImilarity-based GenoTyper), which assigns diploid genotypes by matching read-depth distributions to haplotype paths via cosine similarity. Because this metric evaluates relative coverage profiles rather than absolute read counts, COSIGT substantially outperforms existing likelihood-based tools at low coverage (1-2X). We demonstrate scalability to thousands of modern and ancient genomes, enabling robust, population-scale analyses of complex variation directly from low-coverage datasets.